not at home right now, so i dont know wether this is already possible:

creating notification bubbles not by talking to growl, but by talking to colloquy, so colloquy can decide wether to use growl or its own bubbles, so that there is no growl reliance for 3rd party plugins either

It would be useful to get a list of loaded scripts! Especially to make it clear in what context scripts load - are they global to the whole app or loaded on a per-connection basis? (I guess the former, but it's not at all obvious). I envisage a 'loaded script' class with properties like filename, name, uptime/time loaded...